4ep6: Difference between revisions

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==Crystal structure of the XplA heme domain in complex with imidazole and PEG==
==Crystal structure of the XplA heme domain in complex with imidazole and PEG==
<StructureSection load='4ep6' size='340' side='right' caption='[[4ep6]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
<StructureSection load='4ep6' size='340' side='right'caption='[[4ep6]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4ep6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodococcus_rhodochrous Rhodococcus rhodochrous]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EP6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EP6 FirstGlance]. <br>
<table><tr><td colspan='2'>[[4ep6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_rhodochrous Rhodococcus rhodochrous]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EP6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EP6 FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene><br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2wiv|2wiv]], [[2wiy|2wiy]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr>
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xplA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1829 Rhodococcus rhodochrous])</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ep6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ep6 OCA], [https://pdbe.org/4ep6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ep6 RCSB], [https://www.ebi.ac.uk/pdbsum/4ep6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ep6 ProSAT]</span></td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ep6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ep6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ep6 RCSB], [http://www.ebi.ac.uk/pdbsum/4ep6 PDBsum]</span></td></tr>
</table>
<table>
== Function ==
<div style="background-color:#fffaf0;">
[https://www.uniprot.org/uniprot/Q8GPH7_RHORH Q8GPH7_RHORH]
== Publication Abstract from PubMed ==
The Rhodococcus rhodochrous strain 11Y XplA enzyme is an unusual cytochrome P450-flavodoxin fusion enzyme that catalyzes reductive denitration of the explosive hexahydro-1,3,5-trinitro-1,3,5-triazene (RDX). We show by light scattering that XplA is a monomeric enzyme. XplA has high affinity for imidazole (Kd = 1.6 microM), explaining previous reports of a red-shifted XplA Soret band in pure enzyme. XplA's true Soret maximum is at 417 nm. Similarly, unusually weak XplA flavodoxin FMN binding (Kd = 1.09 microM) necessitates its purification in presence of the cofactor to produce hallmark flavin contributions absent in previously reported spectra. Structural and ligand-binding data reveal a constricted active site able to accommodate RDX and small inhibitory ligands (e.g. 4-phenylimidazole and morpholine) while discriminating against larger azole drugs. The crystal structure also identifies a high affinity imidazole binding site, consistent with its low Kd, and shows active site penetration by PEG, perhaps indicative of an evolutionary lipid metabolizing function for XplA. EPR studies indicate heterogeneity in binding mode for RDX and other ligands. The substrate analogue trinitrobenzene does not induce a substrate-like type I optical shift, but creates a unique low-spin EPR spectrum due to influence on structure around the distal water heme ligand. The substrate-free heme iron potential (-268 mV vs. NHE) is positive for a low-spin P450, and the elevated potential of the FMN semiquinone/hydroquinone couple (-172 mV) is also an adaptation that may reflect (along with absence of a key Thr/Ser residue conserved in oxygen activating P450s) XplA's evolution as a specialized RDX reductase catalyst.
 
Unusual spectroscopic and ligand binding properties of the cytochrome P450-flavodoxin fusion enzyme XplA.,Bui SH, McLean KJ, Cheesman MR, Bradley JM, Rigby SE, Levy CW, Leys D, Munro AW J Biol Chem. 2012 Apr 12. PMID:22500029<ref>PMID:22500029</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Rhodococcus rhodochrous]]
[[Category: Rhodococcus rhodochrous]]
[[Category: Bradley, J M.]]
[[Category: Bradley JM]]
[[Category: Bui, S H.]]
[[Category: Bui SH]]
[[Category: Cheesman, M R.]]
[[Category: Cheesman MR]]
[[Category: Leys, D.]]
[[Category: Leys D]]
[[Category: McLean, K J.]]
[[Category: McLean KJ]]
[[Category: Munro, A W.]]
[[Category: Munro AW]]
[[Category: Rigby, S E.J.]]
[[Category: Rigby SEJ]]
[[Category: Explosive rdx]]
[[Category: Oxidoreductase]]
[[Category: P450 enzyme]]
[[Category: P450 monoxygenase]]

Latest revision as of 18:06, 14 March 2024

Crystal structure of the XplA heme domain in complex with imidazole and PEGCrystal structure of the XplA heme domain in complex with imidazole and PEG

Structural highlights

4ep6 is a 1 chain structure with sequence from Rhodococcus rhodochrous. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.3Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q8GPH7_RHORH

4ep6, resolution 2.30Å

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